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X-RAY DIFFRACTION
Materials and Methods page
4DR5
  •   Crystallization Hide
    Crystallization Experiments
    Method HANGING DROP
    pH 6.5
    Temperature 277.0
    Details MPD, pH 6.5, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 400.51 α = 90
    b = 400.51 β = 90
    c = 175.41 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2011-06-28
     
    Diffraction Radiation
    Monochromator double crystal Si(111) monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.1
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.45
    Resolution(Low) 50
    Number Reflections(All) 184810
    Number Reflections(Observed) 184810
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.123
    B(Isotropic) From Wilson Plot 92.556
     
    High Resolution Shell Details
    Resolution(High) 3.45
    Resolution(Low) 3.54
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.011
    Mean I Over Sigma(Observed) 2.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.45
    Resolution(Low) 19.902
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 184776
    Number of Reflections(Observed) 184776
    Number of Reflections(R-Free) 9323
    Percent Reflections(Observed) 99.97
    R-Factor(Observed) 0.154
    R-Work 0.152
    R-Free 0.1918
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 117.537
    Anisotropic B[1][1] -6.3424
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -6.3424
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 8.715
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.45
    Shell Resolution(Low) 3.489
    Number of Reflections(R-Free) 348
    Number of Reflections(R-Work) 5734
    R-Factor(R-Work) 0.2511
    R-Factor(R-Free) 0.3029
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.489
    Shell Resolution(Low) 3.5298
    Number of Reflections(R-Free) 284
    Number of Reflections(R-Work) 5820
    R-Factor(R-Work) 0.2409
    R-Factor(R-Free) 0.2802
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5298
    Shell Resolution(Low) 3.5727
    Number of Reflections(R-Free) 331
    Number of Reflections(R-Work) 5763
    R-Factor(R-Work) 0.2216
    R-Factor(R-Free) 0.2742
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5727
    Shell Resolution(Low) 3.6176
    Number of Reflections(R-Free) 332
    Number of Reflections(R-Work) 5776
    R-Factor(R-Work) 0.2086
    R-Factor(R-Free) 0.2579
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6176
    Shell Resolution(Low) 3.6649
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 5785
    R-Factor(R-Work) 0.2001
    R-Factor(R-Free) 0.2529
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6649
    Shell Resolution(Low) 3.7148
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 5795
    R-Factor(R-Work) 0.1913
    R-Factor(R-Free) 0.2427
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7148
    Shell Resolution(Low) 3.7675
    Number of Reflections(R-Free) 309
    Number of Reflections(R-Work) 5804
    R-Factor(R-Work) 0.1817
    R-Factor(R-Free) 0.2286
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7675
    Shell Resolution(Low) 3.8234
    Number of Reflections(R-Free) 327
    Number of Reflections(R-Work) 5791
    R-Factor(R-Work) 0.1785
    R-Factor(R-Free) 0.2483
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8234
    Shell Resolution(Low) 3.8827
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 5777
    R-Factor(R-Work) 0.1661
    R-Factor(R-Free) 0.194
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8827
    Shell Resolution(Low) 3.9459
    Number of Reflections(R-Free) 271
    Number of Reflections(R-Work) 5826
    R-Factor(R-Work) 0.1604
    R-Factor(R-Free) 0.2041
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9459
    Shell Resolution(Low) 4.0134
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 5827
    R-Factor(R-Work) 0.1543
    R-Factor(R-Free) 0.1786
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0134
    Shell Resolution(Low) 4.0857
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 5837
    R-Factor(R-Work) 0.1445
    R-Factor(R-Free) 0.1825
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0857
    Shell Resolution(Low) 4.1636
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5829
    R-Factor(R-Work) 0.1481
    R-Factor(R-Free) 0.2141
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1636
    Shell Resolution(Low) 4.2478
    Number of Reflections(R-Free) 326
    Number of Reflections(R-Work) 5770
    R-Factor(R-Work) 0.1477
    R-Factor(R-Free) 0.1696
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2478
    Shell Resolution(Low) 4.3392
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 5821
    R-Factor(R-Work) 0.1439
    R-Factor(R-Free) 0.2074
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3392
    Shell Resolution(Low) 4.4391
    Number of Reflections(R-Free) 319
    Number of Reflections(R-Work) 5841
    R-Factor(R-Work) 0.1471
    R-Factor(R-Free) 0.1935
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4391
    Shell Resolution(Low) 4.5488
    Number of Reflections(R-Free) 270
    Number of Reflections(R-Work) 5860
    R-Factor(R-Work) 0.1416
    R-Factor(R-Free) 0.1879
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5488
    Shell Resolution(Low) 4.6703
    Number of Reflections(R-Free) 306
    Number of Reflections(R-Work) 5837
    R-Factor(R-Work) 0.1342
    R-Factor(R-Free) 0.1898
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6703
    Shell Resolution(Low) 4.8058
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 5851
    R-Factor(R-Work) 0.1307
    R-Factor(R-Free) 0.1802
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8058
    Shell Resolution(Low) 4.9586
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 5866
    R-Factor(R-Work) 0.126
    R-Factor(R-Free) 0.158
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9586
    Shell Resolution(Low) 5.1329
    Number of Reflections(R-Free) 309
    Number of Reflections(R-Work) 5845
    R-Factor(R-Work) 0.1257
    R-Factor(R-Free) 0.1698
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1329
    Shell Resolution(Low) 5.3347
    Number of Reflections(R-Free) 323
    Number of Reflections(R-Work) 5875
    R-Factor(R-Work) 0.1276
    R-Factor(R-Free) 0.1578
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3347
    Shell Resolution(Low) 5.5724
    Number of Reflections(R-Free) 297
    Number of Reflections(R-Work) 5863
    R-Factor(R-Work) 0.1238
    R-Factor(R-Free) 0.1709
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5724
    Shell Resolution(Low) 5.859
    Number of Reflections(R-Free) 311
    Number of Reflections(R-Work) 5888
    R-Factor(R-Work) 0.1199
    R-Factor(R-Free) 0.1534
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.859
    Shell Resolution(Low) 6.2156
    Number of Reflections(R-Free) 338
    Number of Reflections(R-Work) 5851
    R-Factor(R-Work) 0.1252
    R-Factor(R-Free) 0.156
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2156
    Shell Resolution(Low) 6.6786
    Number of Reflections(R-Free) 295
    Number of Reflections(R-Work) 5925
    R-Factor(R-Work) 0.1366
    R-Factor(R-Free) 0.186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6786
    Shell Resolution(Low) 7.3202
    Number of Reflections(R-Free) 304
    Number of Reflections(R-Work) 5948
    R-Factor(R-Work) 0.1325
    R-Factor(R-Free) 0.1843
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.3202
    Shell Resolution(Low) 8.3112
    Number of Reflections(R-Free) 320
    Number of Reflections(R-Work) 5952
    R-Factor(R-Work) 0.1409
    R-Factor(R-Free) 0.1783
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.3112
    Shell Resolution(Low) 10.2289
    Number of Reflections(R-Free) 346
    Number of Reflections(R-Work) 5985
    R-Factor(R-Work) 0.1583
    R-Factor(R-Free) 0.1861
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.2289
    Shell Resolution(Low) 19.9018
    Number of Reflections(R-Free) 348
    Number of Reflections(R-Work) 6111
    R-Factor(R-Work) 0.1863
    R-Factor(R-Free) 0.202
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.8
    f_plane_restr 0.005
    f_chiral_restr 0.061
    f_angle_d 0.869
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19152
    Nucleic Acid Atoms 32880
    Heterogen Atoms 314
    Solvent Atoms 582
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) xds
    Data Reduction (data scaling) XSCALE
    Structure Solution PHENIX (phenix.refine: dev_978)
    Structure Refinement PHENIX (phenix.refine: dev_978)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction Xscale